missed an old figure and moving to zenodo

MoseleyBioinformaticsLab · Mar 1, 2022 · b41d068 · b41d068
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diff --git a/doc/.~lock.ici_kt_manuscript.docx# b/doc/.~lock.ici_kt_manuscript.docx#
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+,rmflight,pop-os.localdomain,01.03.2022 08:48,file:///home/rmflight/.config/libreoffice/4;
diff --git a/doc/ici_kt_manuscript.Rmd b/doc/ici_kt_manuscript.Rmd
@@ -103,7 +103,7 @@ We examine the effect of missing values on simulated data, comparing our informa
 We also evaluate the ability of ICI-Kt to capture outlier samples using three different RNA-seq datasets and comparing to a standard method using Pearson correlation.
 Finally, we examine the ability to recapitulate ICI-Kt correlation values calculated on a large feature omics data set using feature subsets, which is useful when the execution time of very large feature data sets becomes computationally prohibitive.
 
-All of the code used for this manuscript is available on figshare [@flightManuscriptICIKendallTau2022].
+All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2022].
 
 ## Methods
 
@@ -190,7 +190,7 @@ In comparison to directly counting the concordant and discordant pairs, some of
 Therefore, we used 64 bit integers and floats where necessary in the *Rcpp* code.
 
 C++ (via *Rcpp* [@eddelbuettel_rcppseamless_2011; @eddelbuettel_seamlessbook_2013; @eddelbuettel_extendingrcpp_2018]) and R code implementations are in the src/kendallc.cpp and R/kendalltau.R files of the ICIKendallTau R package, hosted at https://github.com/MoseleyBioinformaticsLab/ICIKendallTau.
-The version of the package used in this manuscript is available on figshare [@flightICIKendallTau2022].
+The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2022].
 
 When a large number of samples need to be compared, it may be useful to split the comparisons across compute instances (across hyperthreaded cores, physical cores, or physical compute nodes).
 The *furrr* R package makes the definition of compute clusters easy [@vaughanFurrrApplyMapping2021].
@@ -406,7 +406,6 @@ figure_count$increment("leftcensored")
 ```
 
 ```{r leftcensored, fig.height = 8, fig.width = 8, dn_id = figure_count}
-figure_count$increment("f_leftcensored")
 loadd(left_censored_cor)
 left_censored_cor = left_censored_cor %>%
   dplyr::mutate(which2 = dplyr::case_when(

diff --git a/doc/ici_kt_manuscript.docx b/doc/ici_kt_manuscript.docx
diff --git a/...figure-docx/Figure_11_pearson_nolog-1.png → ...figure-docx/Figure_10_pearson_nolog-1.png b/...figure-docx/Figure_11_pearson_nolog-1.png → ...figure-docx/Figure_10_pearson_nolog-1.png
diff --git a/...ure-docx/Figure_12_pcavardifference-1.png → ...ure-docx/Figure_11_pcavardifference-1.png b/...ure-docx/Figure_12_pcavardifference-1.png → ...ure-docx/Figure_11_pcavardifference-1.png
diff --git a/...files/figure-docx/Figure_13_pcaeval-1.png → ...files/figure-docx/Figure_12_pcaeval-1.png b/...files/figure-docx/Figure_13_pcaeval-1.png → ...files/figure-docx/Figure_12_pcaeval-1.png
diff --git a/...les/figure-docx/Figure_5_singleperf-1.png → ...les/figure-docx/Figure_4_singleperf-1.png b/...les/figure-docx/Figure_5_singleperf-1.png → ...les/figure-docx/Figure_4_singleperf-1.png
diff --git a/...gure-docx/Figure_6_multiperformance-1.png → ...gure-docx/Figure_5_multiperformance-1.png b/...gure-docx/Figure_6_multiperformance-1.png → ...gure-docx/Figure_5_multiperformance-1.png
diff --git a/...figure-docx/Figure_7_yeast_outliers-1.png → ...figure-docx/Figure_6_yeast_outliers-1.png b/...figure-docx/Figure_7_yeast_outliers-1.png → ...figure-docx/Figure_6_yeast_outliers-1.png
diff --git a/...ure-docx/Figure_8_brainson_outliers-1.png → ...ure-docx/Figure_7_brainson_outliers-1.png b/...ure-docx/Figure_8_brainson_outliers-1.png → ...ure-docx/Figure_7_brainson_outliers-1.png
diff --git a/...figure-docx/Figure_9_adeno_outliers-1.png → ...figure-docx/Figure_8_adeno_outliers-1.png b/...figure-docx/Figure_9_adeno_outliers-1.png → ...figure-docx/Figure_8_adeno_outliers-1.png
diff --git a/...igure-docx/Figure_10_icisubsampling-1.png → ...figure-docx/Figure_9_icisubsampling-1.png b/...igure-docx/Figure_10_icisubsampling-1.png → ...figure-docx/Figure_9_icisubsampling-1.png
diff --git a/doc/ici_kt_manuscript_files/figure-docx/brainsonseq_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/brainsonseq_outliers-1.png
diff --git a/doc/icikt_references.json b/doc/icikt_references.json
@@ -2041,7 +2041,7 @@
 		"type": "article",
 		"abstract": "ICIKendallTau version used in the manuscript Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley",
 		"title": "ICIKendallTau",
-		"URL": "https://figshare.com/articles/software/ICIKendallTau/19192886/1",
+		"URL": "https://doi.org/10.5281/zenodo.6311002",
 		"author": [
 			{
 				"family": "Flight",
@@ -2066,7 +2066,7 @@
 		"id": "flightManuscriptICIKendallTau2022",
 		"type": "article",
 		"title": "manuscript.ICIKendallTau",
-		"URL": "https://dx.doi.org/10.6084/m9.figshare.19196645",
+		"URL": "https://dx.doi.org/10.5281/zenodo.6309187",
 		"author": [
 			{
 				"family": "Flight",
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